recipe bioconductor-msexperiment

Infrastructure for Mass Spectrometry Experiments

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MsExperiment.html

License:

Artistic-2.0

Recipe:

/bioconductor-msexperiment/meta.yaml

Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.

package bioconductor-msexperiment

versions:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-protgenerics:

>=1.38.0,<1.39.0

depends bioconductor-qfeatures:

>=1.16.0,<1.17.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-spectra:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dbi:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-msexperiment

and update with::

   mamba update bioconductor-msexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-msexperiment

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-msexperiment:<tag>

(see `bioconductor-msexperiment/tags`_ for valid values for ``<tag>``)

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Link to this page

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